def run_subtool(parser, args):
if args.command == 'combine':
import combine as submodule
elif args.command == 'events':
import events as submodule
elif args.command == 'fasta':
import fasta as submodule
elif args.command == 'fastq':
import fastq as submodule
elif args.command == 'hist':
import hist as submodule
elif args.command == 'nucdist':
import nucdist as submodule
elif args.command == 'occupancy':
import occupancy as submodule
elif args.command == 'qualdist':
import qualdist as submodule
elif args.command == 'readstats':
import readstats as submodule
elif args.command == 'stats':
import stats as submodule
elif args.command == 'tabular':
import tabular as submodule
elif args.command == 'times':
import times as submodule
elif args.command == 'squiggle':
import squiggle as submodule
elif args.command == 'winner':
import winner as submodule
elif args.command == 'yield_plot':
import yield_plot as submodule
# run the chosen submodule.
submodule.run(parser, args)
def main():
"""
Run program
"""
cmn.make_dir(cmn.LOG_DIR)
logging.basicConfig(
# filename=os.path.join(cmn.LOG_DIR, cmn.LOG_FILE_NAME % time.strftime(cmn.LOG_FILE_NAME_TIME)),
handlers=[
logging.FileHandler(
os.path.join(
cmn.LOG_DIR, cmn.LOG_FILE_NAME %
time.strftime(cmn.LOG_FILE_NAME_TIME))),
logging.StreamHandler()
],
level=cmn.LOG_LEVEL,
format=cmn.LOG_MSG_FORMAT,
datefmt=cmn.LOG_TIME_FORMAT)
start_time = time.time()
logging.info("Starting program ...\n")
if "-hmo" in sys.argv:
logging.info(
"Detected 'heatmap only' command line argument, program will use pre-existing combined PTEN correlation file.\n"
)
else:
combine.run()
heatmap.run()
logging.info("Finished running program.")
run_time = time.time() - start_time
logging.info("Total run time: %s.\n" %
time.strftime('%H:%M:%S', time.gmtime(run_time)))
def run_subtool(parser, args):
if args.command == 'combine':
import combine as submodule
elif args.command == 'events':
import events as submodule
elif args.command == 'fasta':
import fasta as submodule
elif args.command == 'fastq':
import fastq as submodule
elif args.command == 'hist':
import hist as submodule
elif args.command == 'nucdist':
import nucdist as submodule
elif args.command == 'occupancy':
import occupancy as submodule
elif args.command == 'qualdist':
import qualdist as submodule
elif args.command == 'readstats':
import readstats as submodule
elif args.command == 'stats':
import stats as submodule
elif args.command == 'tabular':
import tabular as submodule
elif args.command == 'times':
import times as submodule
elif args.command == 'squiggle':
import squiggle as submodule
elif args.command == 'winner':
import winner as submodule
elif args.command == 'yield_plot':
import yield_plot as submodule
# run the chosen submodule.
submodule.run(parser, args)
def run_combine():
import combine
file_list = []
output_path = sys.argv[2]
for i in range(3, len(sys.argv)):
file_list.append(sys.argv[i])
combine.run(output_path, file_list)
def run_combine(output_path, file_list):
import combine
combine.run(output_path, file_list)
def run(self):
combine_to = Path(self.output().path)
combine_to.parent.mkdir(parents=True, exist_ok=True)
combine.run(combine_to, [Path(input_.path) for input_ in self.input()])